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| | <StructureSection load='1k1e' size='340' side='right'caption='[[1k1e]], [[Resolution|resolution]] 1.67Å' scene=''> | | <StructureSection load='1k1e' size='340' side='right'caption='[[1k1e]], [[Resolution|resolution]] 1.67Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1k1e]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1K1E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1k1e]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae_Rd_KW20 Haemophilus influenzae Rd KW20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1E FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.67Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j8d|1j8d]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HI1679 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1e OCA], [https://pdbe.org/1k1e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1e RCSB], [https://www.ebi.ac.uk/pdbsum/1k1e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1e ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1k1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1e OCA], [http://pdbe.org/1k1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1e RCSB], [http://www.ebi.ac.uk/pdbsum/1k1e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1e ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/KDSC_HAEIN KDSC_HAEIN]] Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.<ref>PMID:12639950</ref> | + | [https://www.uniprot.org/uniprot/KDSC_HAEIN KDSC_HAEIN] Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.<ref>PMID:12639950</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Haein]] | + | [[Category: Haemophilus influenzae Rd KW20]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Herzberg, O]] | + | [[Category: Herzberg O]] |
| - | [[Category: Lim, K]] | + | [[Category: Lim K]] |
| - | [[Category: S2F, Structure 2.Function Project]]
| + | |
| - | [[Category: Hi1679]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Kdo 8-p phosphatase]]
| + | |
| - | [[Category: S2f]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| - | [[Category: Structure 2 function project]]
| + | |
| Structural highlights
1k1e is a 12 chain structure with sequence from Haemophilus influenzae Rd KW20. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.67Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
KDSC_HAEIN Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily. Following this observation, a detailed sequence analysis revealed remote homology to two members of the HAD superfamily, the P-domain of Ca(2+) ATPase and phosphoserine phosphatase. The 19-kDa chains of HI1679 form a tetramer both in solution and in the crystalline form. The four monomers are arranged in a ring such that four beta-hairpin loops, each inserted after the first beta-strand of the core alpha/beta-fold, form an eight-stranded barrel at the center of the assembly. Four active sites are located at the subunit interfaces. Each active site is occupied by a cobalt ion, a metal used for crystallization. The cobalt is octahedrally coordinated to two aspartate side-chains, a backbone oxygen, and three solvent molecules, indicating that the physiological metal may be magnesium. HI1679 hydrolyzes a number of phosphates, including 6-phosphogluconate and phosphotyrosine, suggesting that it functions as a phosphatase in vivo. The physiological substrate is yet to be identified; however the location of the gene on the yrb operon suggests involvement in sugar metabolism.
From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.,Parsons JF, Lim K, Tempczyk A, Krajewski W, Eisenstein E, Herzberg O Proteins. 2002 Mar 1;46(4):393-404. PMID:11835514[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wu J, Woodard RW. Escherichia coli YrbI is 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase. J Biol Chem. 2003 May 16;278(20):18117-23. Epub 2003 Mar 14. PMID:12639950 doi:http://dx.doi.org/10.1074/jbc.M301983200
- ↑ Parsons JF, Lim K, Tempczyk A, Krajewski W, Eisenstein E, Herzberg O. From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Proteins. 2002 Mar 1;46(4):393-404. PMID:11835514
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